|
| Status |
Public on Dec 31, 2018 |
| Title |
BAL_SARC_21 |
| Sample type |
RNA |
| |
|
| Source name |
SARC_BAL cells
|
| Organism |
Homo sapiens |
| Characteristics |
diagnosis: SARC
cohort: Freiburg
age (yrs): 39
gender (male=1): 1
cell type: bronchoalveolar lavage (BAL) cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Isolation protocol: BAL cells were obtained by bronchoscopy, immediately isolated and 1 ml of TRIzol was added to the cell pellet, which was then immediately snap frozen in -80 celsius.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized on Affymetrix Whole-Transcript Human Gene 1.0 ST Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using a CGS30007G scanner (serialnumber 54713600)
|
| Description |
HUGENE-1_0-ST-V1 SARC_21
|
| Data processing |
Raw CEL files were RMA normalized using the R/Bioconductor package oligo (V.1.32.0) with default settings. Gene expression data was normalized to the geometric mean of all samples using quantile normalization and expression levels were summarized.
|
| |
|
| Submission date |
Sep 24, 2015 |
| Last update date |
Dec 31, 2018 |
| Contact name |
Antje Prasse |
| Organization name |
Medical School Hannover
|
| Department |
Pneumology
|
| Lab |
Prasse OE6870
|
| Street address |
Carl-Neubergstrasse 1
|
| City |
Hannover |
| ZIP/Postal code |
30625 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10739 |
| Series (2) |
| GSE70867 |
BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells |
| GSE73394 |
BAL cell gene expression is predictive of Mortality in Idiopathic Pulmonary Fibrosis and enriched for Genes of Airway Basal Cells (III) |
|
